plotCorrelationEnrichment: Plot using correlation enrichment from leapR package. A...

In PNNL-CompBio/amlresistancenetworks: Calculates networks that lead to AML resistance to drugs

Plot using correlation enrichment from leapR package. A single plot is saved to the working directory

Description

Plot using correlation enrichment from leapR package. A single plot is saved to the working directory

Usage

plotCorrelationEnrichment(
  exprs,
  geneset,
  fdr.cutoff = 0.05,
  corr.cutoff = 0.1,
  prefix,
  width = 11,
  height = 8.5,
  order.by = "Ingroup mean",
  clean.names = FALSE,
  pathway.plot.size = 3
)

Arguments

exprs	A matrix of intensities with accessions as row names, along with samples in the columns.
geneset	Pathway/Kinase database, eg ncipid, msigdb, both of which are included in leapr.
prefix	string, used for naming the saved plots.
order.by	This determines how the pathways are sorted. Default is pathway correlation of "Ingroup mean", but can also use "BH_pvalue" to sort by significance of the pathways.
clean.names	Boolean, if TRUE removes the "_pathway" ending in pathway names, making the plot easier to read.

PNNL-CompBio/amlresistancenetworks documentation built on Feb. 8, 2025, 11:27 a.m.